Mercurial > repos > saskia-hiltemann > cgatools_v17

annotate tools/cgatools17/mkvcf_v17.xml @ 15:b5c879e950f5 draft default tip

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 402ebee914f2286aa9d98223f501f06c1e4b9c22-dirty
author yhoogstrate
date Fri, 20 Nov 2015 03:50:36 -0500
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1
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1 <tool id="cg_mkvcf" name="Make VCF" version="1.7.1">
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2
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3 <description>Converts masterVar and/or junction files to VCF.</description>
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4
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5 <requirements>
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6 <requirement type="package" version="1">cgatools17</requirement>
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7 </requirements>
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8
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9 <command> <!--run executable-->
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10 cgatools | head -1;
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11 cgatools mkvcf --beta
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12 --reference ${crr.fields.crr_path}
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13 --output $output
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14 $nc
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15 --calibration-root ${crr.fields.calibration_root}
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16 #if $varfiles
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17 #if $junctionfiles <!-- masterVar and SV -->
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18 --source-names masterVar,SV
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19 #for $v in $varfiles
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20 --master-var ${v.input}
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21 #end for
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22 #for $j in $junctionfiles
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23 --junction-file ${j.input}
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24 #end for
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25
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26 #else <!-- masterVar only -->
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27 --source-names masterVar
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28 #for $v in $varfiles
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29 --master-var ${v.input}
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30 #end for
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31 #end if
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32 #else
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33 #if $junctionfiles <!-- SV only -->
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34 --source-names SV
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35 #for $j in $junctionfiles
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36 --junction-file ${j.input}
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37 #end for
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38 #end if
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39 #end if
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40 #if $more_options.options_type_selector == "more"
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41 --junction-score-threshold $jst
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42 --junction-side-length-threshold $jslt
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43 --junction-distance-tolerance $jdt
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44 --junction-length-threshold $jlt
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45 $jnp
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46 $jthc
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47 #end if
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48 </command>
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49
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50 <inputs>
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51 <!-- reference crr -->
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52 <param name="crr" type="select" label="Reference Build">
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53 <options from_data_table="cg_anno_files" />
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54 </param>
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55
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56 <!--form field to select masterVar files-->
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57 <repeat name="varfiles" title="MasterVar files">
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58 <param name="input" type="data" format="tabular" label="Dataset"/>
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59 </repeat>
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60
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61 <!--form field to select junction files-->
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62 <repeat name="junctionfiles" title="Junctions files">
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63 <param name="input" type="data" format="tabular" label="Dataset"/>
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64 </repeat>
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65
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66 <param name="nc" type="boolean" truevalue="--include-no-calls" falsevalue="" selected="False" label="Include no-calls?" help="Include small variants VCF records for loci that are no-called across all input genomes"/>
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67
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68 <!-- advanced settings -->
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69 <conditional name="more_options">
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70 <param name="options_type_selector" type="select" label="Advanced Options">
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71 <option value="hide" selected="True">Hide</option>
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72 <option value="show">Show</option>
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73 </param>
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74 <when value="hide">
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75 <!-- no options -->
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76 </when>
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77 <when value="show">
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78 <param name="jst" type="text" value="10" label="Junction Score Threshold" help="Minimum number of discordant mate pairs for a junction that is required to be labeled as PASS in the FT record"/>
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79 <param name="jslt" type="text" value="70" label="Junction Side Length Threshold" help="Minumum junction side length for a reported junction that is required to be labeled as PASS in the FT record"/>
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80 <param name="jdt" type="text" value="200" label="Junction Distance Tolerance" help="Maximum allowed distance between junctions considered to match (i.e. potentially reflect the same evolutionary event)"/>
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81 <param name="jlt" type="text" value="500" label="Junction Length Threshold" help="Maxumum length between breakpoints terquired to call an intrachromosomal junction"/>
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82 <param name="jnp" type="boolean" truevalue="--junction-normal-priority" falsevalue="" selected="false" label="Junction Normal Priority" help="Normal junction priority for VCF output. Should be used only when comparing two genomes, a tumour and its matched normal"/>
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83 <param name="jthc" type="boolean" truevalue="--junction-tumor-hc" falsevalue="" selected="false" label="Junction Tumour High Confidence" help="Output only high confidence junctions from the second of two genomes. Useful as a means of identifying a set of high-confidence somatic junctions."/>
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84
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85 </when>
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86 </conditional>
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87
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88 <!-- prefix for output file so you dont have to manually rename history items -->
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89 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/>
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90 </inputs>
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91 <outputs>
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92 <data format="vcf" name="output" label="$fname ${tool.name} on ${on_string}"/>
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93 </outputs>
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94
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95
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96 <help>
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97 **What it does**
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98
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99 This tool joins two tab-delimited files based on equal fields or overlapping regions.
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100
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101 **cgatools 1.7.1 Documentation**
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102
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103 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf
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104
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105 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf
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106
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107 **Command line reference**::
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108
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109 COMMAND NAME
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110 mkvcf - Converts var file(s) or masterVar file(s) to VCF.
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111
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112 DESCRIPTION
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113 Converts var file(s) or masterVar file(s) to VCF.
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114
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115 OPTIONS
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116 -h [ --help ]
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117 Print this help message.
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118
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119 --beta
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120 This is a beta command. To run this command, you must pass the --beta
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121 flag.
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122
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123 --reference arg
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124 The reference crr file.
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125
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126 --output arg (=STDOUT)
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127 The output file (may be omitted for stdout).
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128
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129 --field-names arg (=GT,PS,NS,AN,AC,SS,FT,CGA_XR,CGA_FI,GQ,HQ,EHQ,CGA_CEHQ,GL,
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130 CGA_CEGL,DP,AD,CGA_RDP,CGA_ODP,CGA_OAD,CGA_ORDP,CGA_PFAM,
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131 CGA_MIRB,CGA_RPT,CGA_SDO,CGA_SOMC,CGA_SOMR,CGA_SOMS,GT,CGA_GP,
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132 CGA_NP,CGA_CP,CGA_PS,CGA_CT,CGA_TS,CGA_CL,CGA_LS,CGA_SCL,CGA_SLS,
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133 CGA_LAF,CGA_LLAF,CGA_ULAF,GT,FT,CGA_IS,CGA_IDC,CGA_IDCL,CGA_IDCR,
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134 CGA_RDC,CGA_NBET,CGA_ETS,CGA_KES,GT,FT,CGA_BF,CGA_MEDEL,MATEID,
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135 SVTYPE,CGA_BNDG,CGA_BNDGO,CGA_BNDMPC,CGA_BNDPOS,CGA_BNDDEF,CGA_BNDP)
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136 Comma-separated list of field names. By default, all fields are
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137 included, but you may override this option to ensure only a subset of
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138 the fields is included in the VCF output. For a description of each
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139 field, see the cgatools user guide.
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140
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141 --source-names arg (=masterVar,CNV,SV,MEI)
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142 Comma-separated list of source names. The following source names are
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143 available:
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144 masterVar - Includes records extracted from the masterVar file.
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145 CNV - Includes CNV-related records.
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146 SV - Includes records derived from junctions files.
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147 MEI - Includes records describing mobile element insertions.
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148 Some of these source types are only available for more recent pipeline
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149 versions, and some of these source types do not support multi-genome
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150 VCFs. For more information about which source types are available for
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151 which versions of the Complete Genomics pipeline software, see the
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152 cgatools user guide.
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153
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154 --genome-root arg
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155 For each genome to include in the VCF, the genome root directory, for
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156 example /data/GS00118-DNA_A01; this directory is expected to contain
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157 the ASM and LIB subdirectories, for example. You must supply this
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158 option for each genome in the VCF, unless you are using
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159 --source-names=masterVar and you have specified the --master-var option
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160 for each genome in the VCF.
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161
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162 --master-var arg
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163 For each genome to include in the VCF, the masterVar file. If
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164 genome-roots parameter is given, this parameter defaults to the
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165 masterVar in the given genome-root.
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166
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167 --include-no-calls
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168 Small variants VCF records include loci that have no
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169 reference-inconsistent calls.
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170
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171
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172 --calibration-root arg
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173 The directory containing calibration data. For example, there should
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174 exist a file calibration-root/0.0.0/metrics.tsv. This option is only
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175 required if CGA_CEHQ or CGA_CEGL are included in the --field-names
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176 parameter.
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177
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178 --junction-file arg
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179 For each genome to include in the VCF, the junctions file. If
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180 genome-roots parameter is given, this parameter defaults to the
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181 respective junctions file in the export directory.
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182
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183 --junction-score-threshold arg (=10)
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184 Junction score thresholds (discordant mate pair count).
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185
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186 --junction-side-length-threshold arg (=70)
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187 Junction side length threshold.
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188
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189 --junction-distance-tolerance arg (=200)
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190 Distance tolerance for junction compatibility.
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191
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192 --junction-length-threshold arg (=500)
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193 Length threshold for compatible junctions.
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194
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195 --junction-normal-priority
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196 Normal junction priority for vcf output.
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197
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198 --junction-tumor-hc
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199 use high confidence junctions for tumors.
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200
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201
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202 SUPPORTED FORMAT_VERSION
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203 0.3 or later
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204 </help>
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205 </tool>